Volume 12 Supplement 11
Spectral classification of short numerical exon and intron sequences
© Kwan et al; licensee BioMed Central Ltd. 2011
Published: 21 November 2011
This research presents three new numerical representations for classifying short exon and intron sequences using discrete Fourier transform period-3 value. Based on the human genome, results indicate that the Complex Twin-Pair representation is attractive compared with other numerical representations and the approach has potential applications in genome annotation and read mapping.
Current methods for genome annotation focus on sequence similarity or motif matching to known genes and there is a need for a complementary or more effective approach. It is known that protein coding (exonic or C-G rich) regions exhibit a period-3 property which is less prominent in noncoding (intronic or A-T rich) regions. The boundary between these 2 regions becomes less apparent as sequence length becomes shorter. The period-3 property is likely due to the 3-base-length of codons. C-G rich content in coding regions is due to nonuniform codon usage. For spectral analysis of period-3 value, a nucleotide sequence has to be converted to a numerical sequence. The choice of numerical representation affects how well its biological properties can be preserved and reflected.
Based on exon and intron sequences downloaded from UCSC Genome Browser on Human (GRCh37/hg19) (http://genome.ucsc.edu/cgi-bin/hgText) using [1–3], the classification performance in precisions (%) were computed by applying the spectral analysis and thresholding of  to the following twelve numerical representation methods: 1. Integer Number; 2. Single Galois Indicator; 3. Paired Nucleotide Atomic Number; 4. Atomic Number; 5. Molecular Mass; 6. EIIP; 7. Paired Numeric; 8. Real Number; 9. Complex Number; 10. Complex Twin-Pair (C, G = -1; A, T = j); 11. Complex Bipolar-Pair Code I (C = -1; G = 1; A = j; T = -j); 12. Complex Bipolar-Pair Code II (C = -1; G = 1; A = -j; T = j). Methods 1-9 are specified in  and Methods 10-12 are new numerical representations. In simulations, two adjacent windows are overlapped by 3 bases.
Results and conclusions
- Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, Haussler D, Kent WJ: The UCSC Table Browser data retrieval tool. Nucleic Acids Res 2004, 32(Database issue):D493–496.PubMed CentralView ArticlePubMedGoogle Scholar
- Goecks J, Nekrutenko A, Taylor J: Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol 2010, 11(8):R86. 10.1186/gb-2010-11-8-r86PubMed CentralView ArticlePubMedGoogle Scholar
- Blackenberg D, Von Kuster G, Coraor N, Ananda G, Lazarus R, Mangan M, Nekrutenko A, Taylor J: Galaxy: a web-based genome analysis tool for experimentalists. Curr Protoc Mol Biol 2010, Chapter 19(Unit 19.10):1–21.Google Scholar
- Kwan JYY, Kwan BYM, Kwan HK: Spectral analysis of numerical exon and intron sequences. In Proceedings of IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW). Hong Kong; 2010:876–877.View ArticleGoogle Scholar
This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.